Jan-Mathijs Schoffelen, Alexandre Gramfort, John C. Mosher, Matti Stenroos, Caroline Witton, Jukka Nenonen, Amit Jaiswal, Robert Oostenveld, Vladimir Litvak, Lauri Parkkonen, Sarang S. Dalal, Britta U. Westner, Aalto University School of Science and Technology [Aalto, Finland], Megin Oy, Modelling brain structure, function and variability based on high-field MRI data (PARIETAL), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Service NEUROSPIN (NEUROSPIN), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Aarhus University [Aarhus], Wellcome Trust Centre for Neuroimaging, University College of London [London] (UCL), The University of Texas Health Science Center at Houston (UTHealth), Aston University [Birmingham], Donders Institute for Brain, Cognition and Behaviour, Radboud university [Nijmegen], Department of Neuroscience and Biomedical Engineering, Université Paris-Saclay, Aarhus University, University College London, University of Texas Health Science Center at Houston, Radboud University Nijmegen, Aston University, Aalto-yliopisto, Aalto University, HUS Medical Imaging Center, BioMag Laboratory, Department of Diagnostics and Therapeutics, Helsinki University Hospital Area, Service NEUROSPIN (NEUROSPIN), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), and Radboud University [Nijmegen]
Beamformers are applied for estimating spatiotemporal characteristics of neuronal sources underlying measured MEG/EEG signals. Several MEG analysis toolboxes include an implementation of a linearly constrained minimum-variance (LCMV) beamformer. However, differences in implementations and in their results complicate the selection and application of beamformers and may hinder their wider adoption in research and clinical use. Additionally, combinations of different MEG sensor types (such as magnetometers and planar gradiometers) and application of preprocessing methods for interference suppression, such as signal space separation (SSS), can affect the results in different ways for different implementations. So far, a systematic evaluation of the different implementations has not been performed. Here, we compared the localization performance of the LCMV beamformer pipelines in four widely used open-source toolboxes (MNE-Python, FieldTrip, DAiSS (SPM12), and Brainstorm) using datasets both with and without SSS interference suppression. We analyzed MEG data that were i) simulated, ii) recorded from a static and moving phantom, and iii) recorded from a healthy volunteer receiving auditory, visual, and somatosensory stimulation. We also investigated the effects of SSS and the combination of the magnetometer and gradiometer signals. We quantified how localization error and point-spread volume vary with the signal-to-noise ratio (SNR) in all four toolboxes. When applied carefully to MEG data with a typical SNR (3–15 dB), all four toolboxes localized the sources reliably; however, they differed in their sensitivity to preprocessing parameters. As expected, localizations were highly unreliable at very low SNR, but we found high localization error also at very high SNRs for the first three toolboxes while Brainstorm showed greater robustness but with lower spatial resolution. We also found that the SNR improvement offered by SSS led to more accurate localization., Highlights • Different beamformer implementations are reported to sometimes yield differing source estimates for the same MEG data. • We compared beamformers in four major open-source MEG analysis toolboxes. • All toolboxes provide consistent and accurate results with 3–15-dB input SNR. • However, localization errors are high at very high input SNR for the tested scalar beamformers. • We discuss the critical differences between the implementations.